A course at a military academy that taught US officers to prepare for "total war" with Islam does not represent an isolated incident, campaigners have warned.

The Pentagon moved swiftly to distance itself from revelations that officers in a defense department class were taught that "Hiroshima"-style tactics would be needed to combat the threat from Islam.

"It was totally objectionable, against our values and it wasn't academically sound," said General Martin Dempsey, chairman of the joint chiefs of staff.

The class in question was canceled in April and Dempsey noted the instructor responsible for the course, army lieutenant colonel Matthew A Dooley, is "no longer in a teaching status". Dooley, however, is still employed at the Joint Forces Staff College in Norfolk, Virginia.

Linda Sarsour, executive director at the Arab American Association of New York, said the course is merely the latest example in a proliferation of anti-Muslim teaching materials in law-enforcement agencies. "It's part of a much larger problem," Sarsour said, pointing to similar controversies involving the FBI and the New York police department.

On Thursday, Danger Room – a national security blog at Wired.com – published a series of documents revealing that a defense department class for US military officers urged soldiers to prepare for a "total war" against the world's 1.4 billion Muslims. In this battle for supremacy, Geneva Convention standards for armed conflict would be irrelevant and the historical precedents of Dresden, Tokyo, Hiroshima and Nagasaki would be applied to civilian populations "wherever necessary".

Hundreds of pages of teaching material and reference documents obtained by Danger Room show the course – which was open to US military commanders, lieutenant colonels, captains and colonels – argued that the real threat to US national security stemmed not from radical militants, but from Islam itself.

In a July presentation, Dooley claimed: "We have now come to understand that there is no such thing as 'moderate Islam'. It is therefore time for the United States to make our true intentions clear. This barbaric ideology will no longer be tolerated. Islam must change or we will facilitate its self-destruction." He proposed a four-stage solution that included the possibility of reducing Islam to "a cult status" and threatening Saudi Arabia with starvation.

Dooley brought in several ideological allies to support his conclusion, including Shireen Burki, who in 2008 told future military decision makers that "Obama is bin Laden's dream candidate". John Guandolo, a former FBI employee, presented students with an array of materials including a paper in which he argued: "It is a permanent command in Islam for Muslims to hate and despise Jews and Christians."

The course echoes a curriculum presented to FBI agents. In September, FBI whistleblowers provided Danger Room with a trove of the agency's training materials in which counter-terrorism agents were taught that "main stream" [sic] American Muslims are likely to be terrorist sympathizers; that the Prophet Mohammed was a 'cult leader'; and that the Islamic practice of giving charity is no more than a "funding mechanism for combat".

The influence of anti-Islamic rhetoric has also found its way into municipal police departments. The New York police department has been the subject of increasing scrutiny amid a series of reports from the Associated Press revealing the existence of the department's so-called "Demographics Unit", which has been used to map out ethnic communities. The unit focused on a list of 28 "ancestries of interest", all of which are predominantly Muslim. In the course of over two dozen articles, the AP laid out how the NYPD – with the help of CIA advisers – infiltrated mosques, Muslim community centers and local colleges.

In January the New York Times revealed the department had played the Third Jihad – a film which claims that American Muslims of all stripes are in the midst of an effort to seize control of the country – for 1,489 police officers. The NYPD initially denied that any officers had seen the film and that it was not involved in its production, but was eventually forced to admit that police commissioner Ray Kelly participated in an interview for the film.

Sarsour said the latest revelations showed the problem was widespread. "It's not just the department of defense. It's not just the military. It's anywhere from showing a movie like the Third Jihad to 1,500 New York City police officers to training FBI agents that Muslims are easily radicalized to become terrorists."

She said the Islamophobic lessons taught to US military and law enforcement personnel have further damaged national security. "There's already a deficit of trust between the community and law enforcement."

Sarsour argued that such revelations feed the narrative offered by extremist groups. "We're basically confirming what al-Qaida is telling Muslims across the world," she said. "Our government should be up in arms to know that this is happening, particularly at the department of defense, in a very fragile time in the Middle East."